Creating busticated version of OpenMD
Added preliminary code for Alpha Hull calculation using qhull. Added preliminary support to SMIPD to support Alpha Hull. Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. Preliminary changes for shadow hamiltonian integrator. Chages to md files so they will work in openMD.
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
converted samples over to the OOPSE-4 file format Fixed an MPI bug in thermodynamic integration
remove deprecated keywords from samples
uncommented .in line
Import of OOPSE v. 2.0
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